I run a test simulation for -rerun. I didn't change the topology file. grompp -f md.mdp -c solvent-bmi-pf6-128.pdb -p solvent-bmi-pf6-128.top -o 3.tpr mpirun -machinefile cp -np 8 mdrun -s 3.tpr -o 3.trr -c solvent-bmi-pf6-128.pdb -e 3.edr -g 3.log
with -rerun grompp -f md.mdp -c solvent-bmi-pf6-128.pdb -p solvent-bmi-pf6-128.top -o 6.tpr mpirun -machinefile cp -np 8 mdrun -s 6.tpr -o 6.trr -rerun 3.trr -c solvent-bmi-pf6-128.pdb -e 6.edr -g 6.log rm -f *#* I calculate the total energy by g_energy -f 3.edr -o 3.xvg g_energy -f 6.edr -o 6.xvg The total enregy vaies beteen +- 30.00 KJ/mol. It should be constant since I using same topology file and trajectroy. Why the total energy is not contant. NIlesh On Thu, October 21, 2010 10:24 am, Mark Abraham wrote: > On 22/10/2010 1:17 AM, Nilesh Dhumal wrote: > >> I am doing solvation dynamics for my system. >> I have system with diatomic (PA---NE)solute surrounded by water >> molecules. >> >> I want to run simulation with two differcent cases. >> 1. PA charge=0 and NE charge=0 : No charge on solute >> 2. PA charge=+1 and NE charge=-1 : Charge on solute >> >> >> I want to calculate the energy at each step keeping the solvent >> configration same. >> >> IF I start a simulation with no charge on solute (case1), I have the >> energy for 1 step. I want to calculate the energy with charge on solute >> (case 2) with same configration water molecules. >> Each step I want to calculate the energy with and without charge on >> solute since the configration of solvent will be same for that step. >> >> I was thinking two make two topologies file with charge and with out >> charge on solute. I don't know how to use them simultaneously during the >> simulation. > > Well, you don't use them simultaneously. You run a simulation on > whatever you think will generate a relevant conformational ensemble. Then > you want to use mdrun -rerun twice on the resulting trajectory, using .tpr > files based on .top files corresponding to the two cases in order to > create your comparison. > > Mark > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read > http://www.gromacs.org/Support/Mailing_Lists > > > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
